Imputation Report For Cohort: T1DGC_cohort

Per chromosome imputation report for cohort T1DGC_cohort.

Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X

Cohort Metadata

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Information captured during the processing of this cohort.

Property Value
FORMAT MINIMAC2

UPLOADED 12.4.2021

Genome-Wide

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A: Alternate Allele Frequency: Genome-Wide

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 20497001 81.568
0.1 1220470 4.857
0.2 811191 3.228
0.3 617949 2.459
0.4 494996 1.970
0.5 406341 1.617
0.6 350646 1.395
0.7 291635 1.161
0.8 243804 0.970
0.9 194727 0.775
Total 25128760 100.000

B: Imputation INFO Score: Genome-Wide

Variants binned by imputation INFO score

INFO Score Count %
0.3 1268508 5.048
0.4 1503337 5.983
0.5 1965354 7.821
0.6 2654962 10.565
0.7 3458208 13.762
0.8 4034514 16.055
0.9 10192185 40.560
1.0 51692 0.206
Total 25128760 100.000

Chromosome 1

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1536531 81.6889
0.1 89911 4.7801
0.2 57738 3.0696
0.3 45509 2.4195
0.4 37536 1.9956
0.5 30270 1.6093
0.6 27360 1.4546
0.7 21974 1.1682
0.8 18589 0.9883
0.9 15536 0.8260
Total 1880954

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 98971 5.2617
0.4 116931 6.2166
0.5 149567 7.9517
0.6 201924 10.7352
0.7 264384 14.0558
0.8 308052 16.3774
0.9 737693 39.2191
1.0 3432 0.1825
Total 1880954

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 2

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1737956 82.2001
0.1 100876 4.7711
0.2 65593 3.1024
0.3 49851 2.3578
0.4 38518 1.8218
0.5 32920 1.5570
0.6 28768 1.3606
0.7 23263 1.1003
0.8 20210 0.9559
0.9 16344 0.7730
Total 2114299

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 103782 4.9086
0.4 121627 5.7526
0.5 160492 7.5908
0.6 219130 10.3642
0.7 291562 13.7900
0.8 344302 16.2845
0.9 868390 41.0722
1.0 5014 0.2371
Total 2114299

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 3

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1441882 81.5967
0.1 87668 4.9612
0.2 55347 3.1321
0.3 43084 2.4381
0.4 35180 1.9909
0.5 29118 1.6478
0.6 24728 1.3994
0.7 20347 1.1514
0.8 16994 0.9617
0.9 12735 0.7207
Total 1767083

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 84583 4.7866
0.4 100046 5.6616
0.5 132178 7.4800
0.6 181514 10.2720
0.7 241990 13.6943
0.8 288690 16.3371
0.9 733634 41.5167
1.0 4448 0.2517
Total 1767083

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 4

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1386722 80.6895
0.1 82142 4.7796
0.2 60783 3.5368
0.3 45277 2.6345
0.4 33857 1.9700
0.5 28032 1.6311
0.6 24432 1.4216
0.7 21800 1.2685
0.8 20149 1.1724
0.9 15397 0.8959
Total 1718591

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 86883 5.0555
0.4 100717 5.8604
0.5 131753 7.6663
0.6 177622 10.3353
0.7 229368 13.3463
0.8 269697 15.6929
0.9 719191 41.8477
1.0 3360 0.1955
Total 1718591

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 5

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1311159 81.7219
0.1 76716 4.7816
0.2 53094 3.3092
0.3 40002 2.4932
0.4 31533 1.9654
0.5 24557 1.5306
0.6 22449 1.3992
0.7 18435 1.1490
0.8 14780 0.9212
0.9 11690 0.7286
Total 1604415

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 77529 4.8322
0.4 91286 5.6897
0.5 119891 7.4726
0.6 164036 10.2240
0.7 216567 13.4982
0.8 260188 16.2170
0.9 671484 41.8523
1.0 3434 0.2140
Total 1604415

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 6

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1266410 80.9261
0.1 80893 5.1692
0.2 52860 3.3779
0.3 40412 2.5824
0.4 32630 2.0851
0.5 25689 1.6416
0.6 22585 1.4432
0.7 17140 1.0953
0.8 15416 0.9851
0.9 10861 0.6940
Total 1564896

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 71139 4.5459
0.4 83482 5.3347
0.5 108716 6.9472
0.6 150014 9.5862
0.7 203763 13.0209
0.8 246006 15.7203
0.9 697243 44.5552
1.0 4533 0.2897
Total 1564896

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 7

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1160183 81.5374
0.1 69020 4.8507
0.2 47809 3.3600
0.3 35310 2.4816
0.4 28731 2.0192
0.5 23423 1.6462
0.6 19271 1.3544
0.7 16523 1.1612
0.8 12101 0.8505
0.9 10513 0.7389
Total 1422884

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 70931 4.9850
0.4 84267 5.9223
0.5 109725 7.7115
0.6 147366 10.3569
0.7 195005 13.7049
0.8 229592 16.1357
0.9 583204 40.9875
1.0 2794 0.1964
Total 1422884

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 8

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1158266 82.3135
0.1 64353 4.5733
0.2 44659 3.1737
0.3 32120 2.2826
0.4 27540 1.9572
0.5 21624 1.5367
0.6 19123 1.3590
0.7 15687 1.1148
0.8 13368 0.9500
0.9 10399 0.7390
Total 1407139

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 68685 4.8812
0.4 81266 5.7753
0.5 104191 7.4045
0.6 142402 10.1200
0.7 188814 13.4183
0.8 226292 16.0817
0.9 591322 42.0230
1.0 4167 0.2961
Total 1407139

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 9

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 866945 81.7432
0.1 53648 5.0584
0.2 33821 3.1889
0.3 24975 2.3549
0.4 20403 1.9238
0.5 15858 1.4952
0.6 14677 1.3839
0.7 11910 1.1230
0.8 9444 0.8905
0.9 8891 0.8383
Total 1060572

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 49938 4.7086
0.4 58816 5.5457
0.5 77871 7.3424
0.6 107412 10.1277
0.7 143417 13.5226
0.8 173763 16.3839
0.9 447098 42.1563
1.0 2257 0.2128
Total 1060572

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 10

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 993849 81.3531
0.1 60620 4.9621
0.2 39646 3.2453
0.3 28716 2.3506
0.4 24491 2.0048
0.5 20895 1.7104
0.6 17170 1.4055
0.7 13817 1.1310
0.8 12845 1.0514
0.9 9599 0.7857
Total 1221648

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 57938 4.7426
0.4 68419 5.6005
0.5 89902 7.3591
0.6 122118 9.9962
0.7 161919 13.2541
0.8 195719 16.0209
0.9 523011 42.8119
1.0 2622 0.2146
Total 1221648

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 11

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 980869 81.2671
0.1 58975 4.8862
0.2 36448 3.0198
0.3 30686 2.5424
0.4 24302 2.0135
0.5 20869 1.7290
0.6 18004 1.4917
0.7 14215 1.1777
0.8 12166 1.0080
0.9 10435 0.8646
Total 1206969

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 57265 4.7445
0.4 68854 5.7047
0.5 89865 7.4455
0.6 124020 10.2753
0.7 166635 13.8061
0.8 198354 16.4341
0.9 499498 41.3845
1.0 2478 0.2053
Total 1206969

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 12

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 942631 81.4067
0.1 56746 4.9007
0.2 35506 3.0663
0.3 30489 2.6331
0.4 22948 1.9818
0.5 19080 1.6478
0.6 16133 1.3933
0.7 12803 1.1057
0.8 12294 1.0617
0.9 9298 0.8030
Total 1157928

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 57529 4.9683
0.4 68869 5.9476
0.5 90006 7.7730
0.6 122416 10.5720
0.7 158630 13.6995
0.8 182349 15.7479
0.9 475215 41.0401
1.0 2914 0.2517
Total 1157928

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 13

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 699713 80.5303
0.1 43052 4.9549
0.2 27668 3.1843
0.3 22774 2.6211
0.4 17409 2.0036
0.5 15651 1.8013
0.6 12474 1.4356
0.7 11313 1.3020
0.8 9765 1.1239
0.9 9063 1.0431
Total 868882

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 40391 4.6486
0.4 48364 5.5662
0.5 64340 7.4049
0.6 89214 10.2677
0.7 119441 13.7465
0.8 139969 16.1091
0.9 365275 42.0397
1.0 1888 0.2173
Total 868882

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 14

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 646118 81.7158
0.1 39059 4.9399
0.2 26281 3.3238
0.3 18132 2.2932
0.4 15216 1.9244
0.5 11937 1.5097
0.6 9969 1.2608
0.7 9180 1.1610
0.8 8006 1.0125
0.9 6791 0.8589
Total 790689

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 38524 4.8722
0.4 45580 5.7646
0.5 60670 7.6731
0.6 82798 10.4716
0.7 109586 13.8596
0.8 125331 15.8509
0.9 326750 41.3247
1.0 1450 0.1834
Total 790689

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 15

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 567361 81.5638
0.1 33223 4.7761
0.2 22437 3.2255
0.3 16751 2.4081
0.4 14286 2.0538
0.5 11830 1.7007
0.6 8924 1.2829
0.7 7997 1.1496
0.8 6527 0.9383
0.9 6268 0.9011
Total 695604

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 36500 5.2472
0.4 43460 6.2478
0.5 57267 8.2327
0.6 76337 10.9742
0.7 95918 13.7892
0.8 109882 15.7966
0.9 275047 39.5407
1.0 1193 0.1715
Total 695604

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 16

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 627186 81.9464
0.1 38084 4.9760
0.2 22538 2.9448
0.3 19195 2.5080
0.4 14481 1.8920
0.5 11956 1.5621
0.6 10855 1.4183
0.7 9395 1.2275
0.8 6849 0.8949
0.9 4822 0.6300
Total 765361

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 42878 5.6023
0.4 50858 6.6450
0.5 66610 8.7031
0.6 87749 11.4650
0.7 110683 14.4615
0.8 124618 16.2823
0.9 281207 36.7417
1.0 758 0.0990
Total 765361

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 17

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 544682 81.9660
0.1 29996 4.5139
0.2 23116 3.4786
0.3 15483 2.3299
0.4 13350 2.0090
0.5 11230 1.6899
0.6 9032 1.3592
0.7 7860 1.1828
0.8 5872 0.8836
0.9 3901 0.5870
Total 664522

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 39950 6.0118
0.4 47123 7.0913
0.5 61533 9.2597
0.6 80267 12.0789
0.7 98055 14.7557
0.8 106689 16.0550
0.9 230374 34.6676
1.0 531 0.0799
Total 664522

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 18

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 558934 81.1186
0.1 33655 4.8844
0.2 23636 3.4303
0.3 17675 2.5652
0.4 13916 2.0196
0.5 10842 1.5735
0.6 9486 1.3767
0.7 8094 1.1747
0.8 6651 0.9653
0.9 6144 0.8917
Total 689033

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 34412 4.9942
0.4 41282 5.9913
0.5 54101 7.8517
0.6 74408 10.7989
0.7 96358 13.9845
0.8 110728 16.0701
0.9 276533 40.1335
1.0 1211 0.1758
Total 689033

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 19

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 422577 80.7744
0.1 28984 5.5402
0.2 18999 3.6316
0.3 13261 2.5348
0.4 9752 1.8641
0.5 8675 1.6582
0.6 7159 1.3684
0.7 6064 1.1591
0.8 4505 0.8611
0.9 3181 0.6080
Total 523157

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 33034 6.3144
0.4 40283 7.7000
0.5 52204 9.9786
0.6 65538 12.5274
0.7 77403 14.7954
0.8 81502 15.5789
0.9 172909 33.0511
1.0 284 0.0543
Total 523157

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 20

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 448900 81.6759
0.1 27125 4.9353
0.2 18053 3.2847
0.3 13465 2.4499
0.4 11222 2.0418
0.5 8921 1.6231
0.6 7761 1.4121
0.7 5955 1.0835
0.8 4515 0.8215
0.9 3694 0.6721
Total 549611

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 29420 5.3529
0.4 35076 6.3820
0.5 46742 8.5046
0.6 61177 11.1310
0.7 77215 14.0490
0.8 86393 15.7189
0.9 212877 38.7323
1.0 711 0.1294
Total 549611

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 21

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 261202 80.3241
0.1 15945 4.9034
0.2 10347 3.1819
0.3 8982 2.7621
0.4 7142 2.1963
0.5 5864 1.8033
0.6 4976 1.5302
0.7 4405 1.3546
0.8 4099 1.2605
0.9 2223 0.6836
Total 325185

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 17795 5.4723
0.4 21001 6.4582
0.5 27410 8.4290
0.6 36678 11.2791
0.7 45973 14.1375
0.8 50188 15.4337
0.9 125794 38.6838
1.0 346 0.1064
Total 325185

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 22

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 266503 81.5178
0.1 15903 4.8644
0.2 11044 3.3781
0.3 7867 2.4064
0.4 6829 2.0889
0.5 5423 1.6588
0.6 4622 1.4138
0.7 4086 1.2498
0.8 2806 0.8583
0.9 1843 0.5637
Total 326926

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 18930 5.7903
0.4 23024 7.0426
0.5 29219 8.9375
0.6 37633 11.5112
0.7 45307 13.8585
0.8 49826 15.2408
0.9 122356 37.4262
1.0 631 0.1930
Total 326926

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome X

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 670422 83.5508
0.1 33876 4.2218
0.2 23768 2.9621
0.3 17933 2.2349
0.4 13724 1.7103
0.5 11677 1.4552
0.6 10688 1.3320
0.7 9372 1.1680
0.8 5853 0.7294
0.9 5099 0.6355
Total 802412

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 51501 6.4183
0.4 62706 7.8147
0.5 81101 10.1072
0.6 103189 12.8599
0.7 120215 14.9817
0.8 126384 15.7505
0.9 256080 31.9138
1.0 1236 0.1540
Total 802412

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering